Hi, I suggest considering Atomic Simulation Environment (ASE) as the MD driver. It is interfaced to several compute codes via a Calculator object, which computes energy and forces - you would need to implement your own Calculator which would communicate with your Fortran code.
Best,
Michal

Thank you! It turned out to be relatively simple. Just in case anyone else needs a xyz trajectory with units of their choice, this is how I eventually did it: class XyzReporter(object): def __init__(self, file, reportInterval): self._reportInterval = reportInterval self._out = None self.fname = file...

Hello, I would like to save a trajectory with both positions and velocities of all particles. Ideally, in XYZ or GRO format (or something that can be converted to any of these). Is it possible or do I have to write my own reporter? So far, I tried the MdcrdReporter from Parmed, but its format is not...

One more question: what is the default unit of polarizability?

But I would like to keep interactions between two atoms from the same molecule and a third atom from another. Pairwise definition of exclusions would not allow it. I mean if p1 and p2 belong to the same molecule, (p1,p2,p3) is always excluded, regardless of whether p3 belongs to the same molecule (w...

Hi, Im using CustomManyParticleForce to implement a three-body potential. Is it possible to specify exclusions in such a way that this force is evaluated only for intermolecular interactions? I mean excluding all (p1, p2, p3) where p1, p2 and p3 are in the same molecule.

Thank you, this is great! When exactly is this code executed?

I still can't get this right. At the moment, I have a CustomNonbondedForce with bondCutoff=3 and a NonbondedForce which handles Coulomb interactions (1-4 interactions are scaled by 0.5). Now, I would like to add 1-4 interactions to the CustomNonbondedForce (scaled by 0.5, or unscaled). Is it possibl...

Hi,
Is it possible to use vibrational frequencies target with OpenMM? Or any other way to do a Hessian fit?
Thanks,
Michal

Thank you!